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CHECK report for M3D on tokay2

This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE M3D PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 965/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.22.0
Tom Mayo
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/M3D
Branch: RELEASE_3_11
Last Commit: 09ed714
Last Changed Date: 2020-04-27 14:42:10 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3D
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:M3D.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings M3D_1.22.0.tar.gz
StartedAt: 2020-10-17 05:34:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:39:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 286.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: M3D.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:M3D.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings M3D_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'M3D/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'M3D' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'M3D' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
M3D_Wrapper: no visible global function definition for 'txtProgressBar'
M3D_Wrapper: no visible global function definition for
  'setTxtProgressBar'
M3D_Wrapper_lite: no visible global function definition for
  'txtProgressBar'
M3D_Wrapper_lite: no visible global function definition for
  'setTxtProgressBar'
plotCoverageSampleProfiles: no visible global function definition for
  'lines'
plotCoverageSampleProfiles: no visible global function definition for
  'points'
plotCoverageSampleProfiles: no visible global function definition for
  'title'
plotMethProfile: no visible global function definition for 'lines'
plotMethProfile: no visible global function definition for 'points'
plotMethProfile: no visible global function definition for 'title'
plotMethSampleProfiles: no visible global function definition for
  'lines'
plotMethSampleProfiles: no visible global function definition for
  'points'
plotMethSampleProfiles: no visible global function definition for
  'title'
pvals: no visible global function definition for 'p.adjust'
pvals_lite: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  lines p.adjust points setTxtProgressBar title txtProgressBar
Consider adding
  importFrom("graphics", "lines", "points", "title")
  importFrom("stats", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/M3D/libs/x64/M3D.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck/00check.log'
for details.



Installation output

M3D.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch M3D
###
##############################################################################
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* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'M3D' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_fns.cpp -o cpp_fns.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o M3D.dll tmp.def RcppExports.o cpp_fns.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.11-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/R/library/00LOCK-M3D/00new/M3D/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'M3D'
    finding HTML links ... done
    CpGsDemo                                html  
    M3D-package                             html  
    M3D_Single                              html  
    M3D_Wrapper                             html  
    M3D_Wrapper_lite                        html  
    MMDlistDemo                             html  
    PDemo                                   html  
    determineGroupComps                     html  
    findComps                               html  
    medianFreq                              html  
    median_freq                             html  
    plotCoverageSampleProfiles              html  
    plotMethProfile                         html  
    plotMethSampleProfiles                  html  
    pvals                                   html  
    pvals_lite                              html  
    readBedFiles                            html  
    readBedRaw                              html  
    rrbsDemo                                html  
    test_colData_structure                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (M3D)
Making 'packages.html' ... done

Tests output

M3D.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(M3D)
Warning message:
Package 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12 
> 
> test_check("M3D")

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== testthat results  ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.40    0.68   17.09 

Example timings

M3D.Rcheck/M3D-Ex.timings

nameusersystemelapsed
M3D_Wrapper1.380.021.39
M3D_Wrapper_lite0.220.000.22
determineGroupComps0.450.030.49
findComps0.360.050.40
median_freq000
plotCoverageSampleProfiles0.350.000.34
plotMethProfile0.250.000.25
plotMethSampleProfiles0.230.010.25
pvals0.630.050.67
pvals_lite0.440.000.44
readBedFiles000
readBedRaw000